Background: To compare the clinical outcomes of transepithelial photorefractive keratectomy (TPRK) with femtosecond laser-assisted in situ keratomileusis (FS-LASIK) for correction of high myopia. Methods: In this prospective, non-randomised, cohort study, 85 eyes of 46 patients treated with TPRK and 80 eyes of 42 patients treated with FS-LASIK were included. All eyes were highly myopic (spherical equivalent refraction <− 6.00 diopters). Both TPRK and FS-LASIK were performed by Schwind Amaris 750S excimer laser. Visual acuity, refraction, corneal high order aberration (HOA) and other variables were analyzed before and at 1, 3, 6, 12 months after surgery. Results: At 12 months after surgery, uncorrected logMAR distance visual acuity (UDVA) in the TPRK and FS-LASIK groups was − 0.04 ± 0.04 and − 0.01 ± 0.08, respectively (P = 0.039). Corrected logMAR distance visual acuity (CDVA) was − 0.06 ± 0.05 and − 0.04 ± 0.05 in both groups (P = 0.621). For UDVA, 86% of eyes in the TPRK group and 80% in the FS-LASIK group remained unchanged or improved one or more logMAR lines (P = 0.314), compared to preoperative CDVA. For CDVA, 97% of eyes in the TPRK group and 90% in the FS-LASIK group remained unchanged or improved one or more lines (P = 0.096), compared to preoperative CDVA. Spherical equivalent refraction was − 0.05 ± 0.39 and − 0.26 ± 0.47 in both groups (P = 0.030). 87% of eyes in the TPRK group and 73% in the FS-LASIK group achieved ±0.50 D target refraction (P = 0.019). All 85 eyes (100%) in the TPRK group and 75 eyes (92%) in the FS-LASIK group were within ±1.00 D of target (P = 0.003). Root mean square (RMS) of corneal total HOA and vertical coma in the TPRK group were lower compared with the FS-LASIK group (P < 0.001 for both variables). Conclusions: TPRK and FS-LASIK showed good safety, efficacy and predictability for correction of high myopia. Clinical outcomes of TPRK were slightly better than FS-LASIK.